protein binding

Summary

Summary: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.

..In fact, p62 bodies and these structures are indistinguishable. Taken together, our results clearly suggest that p62 is required both for the formation and the degradation of polyubiquitin-containing bodies by autophagy...

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Ewan BirneyNature 447:799-816. 2007

..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...

..The next steps in promoter analysis can be tackled only with reliable predictions, e.g. finding phylogenetically conserved patterns or identifying higher order combinations of sites in promoters of co-regulated genes...

Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists

..The most surprising observation is a major displacement of the α-helical domain of Gαs relative to the Ras-like GTPase domain. This crystal structure represents the first high-resolution view of transmembrane signalling by a GPCR...

..These data establish proof-of-concept for targeting protein-protein interactions of epigenetic 'readers', and provide a versatile chemical scaffold for the development of chemical probes more broadly throughout the bromodomain family...

..During recovery from DNA damage, maximal Mdm2 induction coincides with rapid p53 loss. We propose that the Mdm2-promoted degradation of p53 provides a new mechanism to ensure effective termination of the p53 signal...

Molecular chaperones in the cytosol: from nascent chain to folded protein

..The TLR4-MD-2-LPS structure illustrates the remarkable versatility of the ligand recognition mechanisms employed by the TLR family, which is essential for defence against diverse microbial infection...

..New efforts are being made to abstract knowledge, both computationally and manually, about ortholog clusters in the KO (KEGG Orthology) database, and to collect and analyze carbohydrate structures in the GLYCAN database...

..In contrast, expression of a catalytically inactive hSir2 protein potentiates p53-dependent apoptosis and radiosensitivity. We propose that hSir2 is involved in the regulation of p53 function via deacetylation...

..Our data suggest that RPA-coated ssDNA is the critical structure at sites of DNA damage that recruits the ATR-ATRIP complex and facilitates its recognition of substrates for phosphorylation and the initiation of checkpoint signaling...

..The results define a framework for understanding regulatory factor-genome interactions and provide a molecular basis for the tissue selectivity of steroid pharmaceuticals and other agents that intersect the living genome...

..96] and statistical confidence (P <10(-4)), properties that were important for inferring new candidate interactions. These include key transcription factors in the gene network that regulates pancreatic islet cell development...

..In particular, nuclear proteins and proteins involved in regulating metabolic processes have high phosphorylation site occupancy in mitosis. This suggests that these proteins may be inactivated by phosphorylation in mitotic cells...

..The Rag proteins do not directly stimulate the kinase activity of mTORC1, but, like amino acids, promote the intracellular localization of mTOR to a compartment that also contains its activator Rheb...

TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing

..Thus beta-catenin regulates gene expression by direct interaction with transcription factors such as LEF-1, providing a molecular mechanism for the transmission of signals, from cell-adhesion components or wnt protein to the nucleus...

..We describe the conformational changes in both ribosomal subunits that are involved in ratcheting and their implications in coordination between the two associated subunits and in mRNA and tRNA translocation...

The transcription factor snail is a repressor of E-cadherin gene expression in epithelial tumour cells

..We also analyze the relationship between the depth of sequencing and characteristics of the detected binding positions, and provide a method for estimating the sequencing depth necessary for a desired coverage of protein binding sites.

..Histone marks affect splicing outcome by influencing the recruitment of splicing regulators via a chromatin-binding protein. These results outline an adaptor system for the reading of histone marks by the pre-mRNA splicing machinery...

..These results have significant implications regarding an important role for Sir2alpha in modulating the sensitivity of cells in p53-dependent apoptotic response and the possible effect in cancer therapy...

Dynamic interaction of BiP and ER stress transducers in the unfolded-protein response

A BertolottiSkirball Institute of Biomolecular Medicine, Departments of Medicine and Cell Biology and the Kaplan Cancer Center, New York University School of Medicine, New York, New York 10016, USANat Cell Biol 2:326-32. 2000

..These findings are consistent with a model in which BiP represses signalling through PERK and IRE1 and protein misfolding relieves this repression by effecting the release of BiP from the PERK and IRE1 lumenal domains...

..Our results indicate that APP and DR6 are components of a neuronal self-destruction pathway, and suggest that an extracellular fragment of APP, acting via DR6 and caspase 6, contributes to Alzheimer's disease...

..This effect decreases the likelihood of cross talk between different functional modules of the cell and increases the overall robustness of a network by localizing effects of deleterious perturbations...

..In light of the new model we discuss details of the tubulin structure such as nucleotide and taxol binding sites, lateral contacts in zinc-sheets, and the significance of the location of highly conserved residues...

..ChIP-seq targets were enriched in sequences similar to known STAT1 binding motifs. Comparisons with two ChIP-PCR data sets suggested that ChIP-seq sensitivity was between 70% and 92% and specificity was at least 95%...

Daniel J HoganDepartment of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of AmericaPLoS Biol 6:e255. 2008

..These results strongly suggest that combinatorial binding of RBPs to specific recognition elements in mRNAs is a pervasive mechanism for multi-dimensional regulation of their post-transcriptional fate...

..In vivo knock-down and in vitro reconstitution studies revealed that both components of this smaller complex, termed Microprocessor, are necessary and sufficient in mediating the genesis of miRNAs from the primary miRNA transcript...

..RAP1 binding at the core region is unaffected by SIR3 overproduction and RAP1 shows no evidence of spreading. Thus, we propose that the structure of core telomeric heterochromatin differs from that extended by SIR3...

..Consequently, the BiFC approach should significantly facilitate the visualization of the subcellular sites of protein interactions under conditions that closely reflect the normal physiological environment...

..of vesicle-associated motors and regulatory factors;(Project 2) identification and characterization of protein binding partners for connexin 32 that may regulate its trafficking to and from the plasma membrane;(Project 3) ..

..identified the replication origin 5'to the human c-myc oncogene, and we have shown that the structure, protein binding and function of the core c-myc replicator as a replication origin are the same at its endogenous chromosomal ..

..and 3 null cells;and deletion of DNA regulatory elements such as the Hoxa1 RARE, followed by analysis of PcG protein binding. We also propose a comparison of 3T3 cells with H-Ras transformed 3T3 cells to assess how an oncogenic ..

..further characterization of the mouse anti-human OX40 antibody variable regions for specificity of OX40 protein binding (ELISA and Western blot) and insertion of the variable regions from the antibody into an IgG backbone...

..These studies wil provide important insight into the mechanisms controling post-MI neovascularization, and may lead to the development of novel therapeutic approaches for treating ischemic heart disease in humans. ..

..Aim #2: Determine the functional domain in ADAR1 that binds to IKK2 and regulates NF-kB activities. The protein binding domain of ADAR1 will be determined through expressions of mutated and truncated ADAR1 in mammalian cells and ..

..ds) DNA aptamers with the sequence domain for AP-1 protein will function as decoys for endogenous AP-1 protein binding. The aptamers will be linked to an MR-visible contrast agent (superparamagnetic iron oxide nanoparticles-..

..expression for key cell cycle TgAP2 proteins, by discovering the promoters they regulate through whole-genome protein binding studies, and by validating the in vivo function of these proteins in parasite replication through the ..

..training will be acquired in applied biophysical protein analysis (including structural, functional, and protein binding assays) through the Center for Structural Biology at the University of North Carolina at Chapel Hill (UNC)...

..The proposed research will enable the development of new strategies to prevent cochlear uptake of cisplatin and its derivates and subsequent ototoxic sequelae, particularly life-long deafness, tinnitus and vestibular deficits. ..

..proliferation, viability and motility of cultured corneal endothelial cells;and demonstrating using DNA-protein binding assays and transfection of an immortalized corneal endothelial cell line that ZEB1-mediated repression of ..

..These candidates include the PRE sequences recognized by Polycomb Group proteins, polymers of the Zeste protein binding site, repeats of the AG dinucleotide recognized by the GAGA protein (the product of the Trithorax-like gene), ..

..the pharmacological properties of SQ609: stability evaluation in plasma and liver microsomes and plasma protein binding of SQ609;determination of pharmacokinetic parameters of SQ609 and bioavailability in mice following both IV ..

..A similar analysis of the complex of ribosomal protein L5 with 5S rRNA will be undertaken. This affords the opportunity to examine the binding of two proteins, that exhibit no sequence identity, to congruent sites on an RNA molecule. ..

..Our preliminary studies point out to exciting properties associated with HSGAG upon protein binding. While the overall helical structure is maintained in the protein-bound HSGAGs, a "kink" in the helical axis ..

..Successful completion of the proposed research will have identified a new drug candidate that can be further developed for prevention and treatment of HBV/HCV induced liver diseases and/or HCC in humans. ..